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comparison arriba_draw_fusions.xml @ 0:2d4e3aff9dc7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
author iuc
date Wed, 27 Jul 2022 11:25:43 +0000
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-1:000000000000 0:2d4e3aff9dc7
1 <tool id="arriba_draw_fusions" name="Arriba Draw Fusions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[
9 #if $alignments.extension == 'sam'
10 ln -sf '$genome.assembly' genome.fa &&
11 samtools faidx genome.fa &&
12 samtools view -b -@ \${GALAXY_SLOTS:-1} -t genome.fa.fai '$alignments' |
13 samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o Aligned.sortedByCoord.out.bam &&
14 samtools index Aligned.sortedByCoord.out.bam &&
15 #else
16 ln -sf '${alignments}' 'Aligned.sortedByCoord.out.bam' &&
17 ln -sf '$alignments.metadata.bam_index' 'Aligned.sortedByCoord.out.bam.bai' &&
18 #end if
19 @DRAW_FUSIONS@
20 ]]></command>
21 <inputs>
22 <param argument="--fusions" type="data" format="tabular" label="Arriba fusions.tsv"/>
23 <param argument="--alignments" type="data" format="sam,bam" label="STAR Aligned.out.bam"/>
24 <expand macro="genome_source" assembly_optional="true"/>
25 <expand macro="gtf_source"/>
26 <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
27 <section name="visualization" expanded="true" title="Visualization Options">
28 <expand macro="visualization_options" />
29 </section>
30 </inputs>
31 <outputs>
32 <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"/>
33 </outputs>
34 <tests>
35 <!-- Test 1 - From SAM -->
36 <test>
37 <param name="fusions" ftype="tabular" value="fusions.tsv"/>
38 <param name="alignments" ftype="sam" value="Aligned.out.sam"/>
39 <conditional name="genome">
40 <param name="genome_source" value="history"/>
41 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
42 </conditional>
43 <conditional name="genome_gtf">
44 <param name="gtf_source" value="history"/>
45 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
46 </conditional>
47 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
48 <section name="visualization">
49 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
50 </section>
51 <output name="fusions_pdf">
52 <assert_contents>
53 <has_size value="64000" delta="5000" />
54 </assert_contents>
55 </output>
56 </test>
57 <!-- Test 2 - From BAM -->
58 <test>
59 <param name="fusions" ftype="tabular" value="fusions.tsv"/>
60 <param name="alignments" ftype="bam" value="Aligned.out.bam"/>
61 <conditional name="genome">
62 <param name="genome_source" value="history"/>
63 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
64 </conditional>
65 <conditional name="genome_gtf">
66 <param name="gtf_source" value="history"/>
67 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
68 </conditional>
69 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
70 <section name="visualization">
71 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
72 </section>
73 <section name="options">
74 <param name="sampleName" value="My Test"/>
75 </section>
76 <output name="fusions_pdf">
77 <assert_contents>
78 <has_size value="64000" delta="5000" />
79 </assert_contents>
80 </output>
81 </test>
82
83 </tests>
84 <help><![CDATA[
85 **Arriba Draw Fusions**
86
87 Arriba_Draw_Fusions_ (draw_fusions.R) renders publication-quality visualizations of the transcripts involved in predicted fusions. It generates a PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and - if the column fusion_transcript has a value - an excerpt of the sequence around the breakpoint.
88
89
90 **INPUTS**
91
92 See: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr
93
94 - Fusions
95
96 File containing fusion predictions from Arriba_ (fusions.tsv) or STAR-Fusion (star-fusion.fusion_predictions.tsv or star-fusion.fusion_predictions.abridged.coding_effect.tsv).
97
98 - Annotation
99
100 Gene annotation in GTF format that was used by the STAR aligner.
101
102 - Alignments
103
104 BAM file containing normal alignments from STAR.
105
106 - Annotation
107
108 The gene annotation (parameter -g) is used for multiple purposes:
109
110 - Assembly (Optional)
111
112 Only required when alignments are not sorted bam format. The genonme assembly will be used by samtools to produce a sorted bam file.
113
114 - Protein domains (Optional)
115
116 GFF3 file containing the genomic coordinates of protein domains. Distributions of Arriba offer protein domain annotations for all supported assemblies in the database directory. When this file is given, a plot is generated, which shows the protein domains retained in the fusion transcript.
117
118 - Cytobands (Optional)
119
120 Coordinates of the Giemsa staining bands. This information is used to draw ideograms. If the argument is omitted, then no ideograms are rendered. The file must have the following columns: contig, start, end, name, giemsa. Recognized values for the Giemsa staining intensity are: gneg, gpos followed by a percentage, acen, stalk. Cytobands forahuman and mouse reference can be retrieved from the Arriba distribution with the **Arriba Get Filters** tool.
121
122
123 **OPTIONS**
124
125 See: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr
126
127
128 **OUTPUTS**
129
130 See: https://arriba.readthedocs.io/en/latest/visualization/
131
132 - fusions.pdf
133
134 A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint.
135
136 .. image:: draw-fusions-example.png
137 :width: 800
138 :height: 467
139
140
141
142
143 .. _Arriba_Draw_Fusions: https://arriba.readthedocs.io/en/latest/visualization/
144 .. _Arriba: https://arriba.readthedocs.io/en/latest/
145
146 ]]></help>
147 <expand macro="citations" />
148 </tool>